US2023031818A1PendingUtilityA1

Methods and compositions for treating colorectal cancer

Assignee: SECOND GENOME INCPriority: Jan 17, 2020Filed: Jan 15, 2021Published: Feb 2, 2023

Est. expiryJan 17, 2040(~13.5 yrs left)· nominal 20-yr term from priority

Inventors:Jayamary Divya Ravichandar Todd Zachary Desantis

G01N 33/57535A61K 9/0031C12Q 1/6886A61P 35/00A61K 35/74C12Q 2600/112A61K 9/20C12Q 1/689A61K 35/742Y02A50/30C12Q 2600/158A61K 35/744C12Q 1/04

PatentIndex Score

Cited by

References

Claims

Abstract

Methods and compositions are provided herein for treating colorectal cancer in a subject, using one or more bacterial strains such as Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482, Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353, Megamonas funiformis DSM 19343, Megasphaera elsdenii LC1, Parabacteroides johnsonii M-165, Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3, Methanosphaera stadtmanae MCB-3, Ruminococcus sp. 18P13, Slackia piriformis DSM 22477, or Streptococcus hongkongensis HKU30.

Claims

exact text as granted — not AI-modified

What is claimed is:

1 . A method of identifying a subject as having colorectal cancer, the method comprising:
(a) identifying a subject having a sample that has: (i) an increased level of one or more bacterial species selected from the group consisting of: Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile , and Veillonella alcalescens ; and/or (ii) a decreased level of one or more bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis , and Streptococcus hongkongensis , as having colorectal cancer; or (b) identifying a subject having a sample that does not have: (i) an increased level of one or more bacterial species selected from the group consisting of: Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile , and Veillonella alcalescens ; and/or (ii) a decreased level of one or more bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis , and Streptococcus hongkongensis , as not having colorectal cancer.

2 . A method of diagnosing a subject as having colorectal cancer, the method comprising:
(a) identifying a subject having a sample that has: (i) an increased level of one or more bacterial species selected from the group consisting of: Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile , and Veillonella alcalescens ; and/or (ii) a decreased level of one or more bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis , and Streptococcus hongkongensis , as having colorectal cancer; or (b) identifying a subject having a sample that does not have: (i) an increased level of one or more bacterial species selected from the group consisting of: Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile, Veillonella alcalescens ; and/or (ii) a decreased level of one or more bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis , and Streptococcus hongkongensis , as not having colorectal cancer.

3 . A method for treating a subject in need thereof, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, and a combination thereof.

4 . The method of claim 3 , wherein the subject has colorectal cancer.

5 . A method for treating colorectal cancer in a subject, the method comprising administering to the subject a composition comprising an effective amount of a bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis, Streptococcus hongkongensis , and a combination thereof.

6 . A method for treating colorectal cancer in a subject, the method comprising:
(a) detecting a dysbiosis associated with colorectal cancer in a sample from the subject; and (b) administering to the subject a composition comprising an effective amount of a bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis, Streptococcus hongkongensis , and a combination thereof.

7 . The method of claim 6 , wherein the sample is a fecal sample.

8 . The method of claim 6 , wherein the sample is a biopsy sample.

9 . The method of claim 8 , wherein the biopsy sample is a colorectal biopsy sample.

10 . The method of any one of claims 6 - 9 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining bacterial gene expression in the sample from the subject.

11 . The method of any one of claims 6 - 10 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining bacterial composition in the sample from the subject.

12 . The method of claim any one of claims 6 - 11 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining that Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile, Veillonella alcalescens , or a combination thereof, is increased in the sample from subject.

13 . The method of claim any one of claims 6 - 12 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining that Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis, Streptococcus hongkongensis , or a combination thereof, is decreased in the sample from subject.

14 . The method of claim 13 , wherein Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis, Streptococcus hongkongensis , or a combination thereof, is decreased in the gastrointestinal tract of the subject.

15 . A method for treating a subject in need thereof, the method comprising decreasing a population of an increased bacterial strain in the subject, wherein the increased bacterial species is selected from the group consisting of: Alistipes indistinctus, Azotobacter sp., Bacteroides asaccharolyticus, Bacteroides sp., Bilophila wadsworthia, Clostridium aldenense, Clostridium bolteae, Clostridium lactatifermentans, Clostridium sp., Desulfovibrio piger, Dialister pneumosintes, Eubacterium biforme, Fusobacterium mortiferum, Hungatella hathewayi, Megasphaera micronuciformis, Micromonas micros, Paraprevotella clara, Peptostreptococcus stomatis, Porphyromonas somerae, Roseburia inulinivorans, Ruminococcus gnavus, Shigella dysenteriae, Subdoligranulum variabile, Veillonella alcalescens , and a combination thereof.

16 . The method of claim 15 , wherein the subject has colorectal cancer.

17 . The method of claim 15 or 16 , wherein decreasing the population of an increased bacterial strain comprises administering to the subject a bacteriophage.

18 . The method of any one of claims 15 - 17 , wherein decreasing the population of an increased bacterial species comprises administering to the subject a composition comprising an effective amount of a bacterial species selected from the group consisting of: Bacteroides eggerthii, Bacteroides eggerthii, Bacteroides goldsteinii, Bacteroides pectinophilus, Bacteroides plebeius, Bacteroides vulgatus, Barnesiella intestinihominis, Bifidobacterium stercoris, Clostridium sp., Clostridium spiroforme, Eubacterium eligens, Eubacterium hallii, Megamonas funiformis, Megasphaera elsdenii, Parabacteroides johnsonii, Butyricimonas virosa, Clostridium citroniae, Lactobacillus ruminis, Methanosphaera stadtmanae, Ruminococcus sp., Slackia piriformis, Streptococcus hongkongensis , and a combination thereof.

19 . The method of any one of claims 1 , 2 , 4 - 14 , and 16 - 18 , wherein the colorectal cancer is adenocarcinoma, a carcinoid tumor, a gastrointestinal stromal tumor, or lymphoma.

20 . The method of any one of claims 1 - 14 , 18 , and 19 , wherein the bacterial species Bacteroides eggerthii comprises the strain Bacteroides eggerthii 1 2 48FAA.

21 . The method of any one of claims 1 - 14 and 18 - 20 , wherein the bacterial species Bacteroides eggerthii comprises the strain Bacteroides eggerthii CCUG 9559.

22 . The method of any one of claims 1 - 14 and 18 - 21 , wherein the bacterial species Bacteroides goldsteinii comprises the strain Bacteroides goldsteinii ATCC BAA 1180.

23 . The method of any one of claims 1 - 14 and 18 - 22 , wherein the bacterial species Bacteroides pectinophilus comprises the strain Bacteroides pectinophilus N3.

24 . The method of any one of claims 1 - 14 and 18 - 23 , wherein the bacterial species Bacteroides plebeius comprises the strain Bacteroides plebeius M12.

25 . The method of any one of claims 1 - 14 and 18 - 24 , wherein the bacterial species Bacteroides vulgatus comprises the strain Bacteroides vulgatus 8482.

26 . The method of any one of claims 1 - 14 and 18 - 25 , wherein the bacterial species Barnesiella intestinihominis comprises the strain Barnesiella intestinihominis DSM 21032.

27 . The method of any one of claims 1 - 14 and 18 - 26 , wherein the bacterial species Bifidobacterium stercoris comprises the strain Bifidobacterium stercoris EG1.

28 . The method of any one of claims 1 - 14 and 18 - 27 , wherein the bacterial species Clostridium sp. comprises the strain Clostridium sp. 40.

29 . The method of any one of claims 1 - 14 and 18 - 28 , wherein the bacterial species Clostridium spiroforme comprises the strain Clostridium spiroforme CCM 6168.

30 . The method of any one of claims 1 - 14 and 18 - 29 , wherein the bacterial species Eubacterium eligens comprises the strain Eubacterium eligens DSM 3376.

31 . The method of any one of claims 1 - 14 and 18 - 30 , wherein the bacterial species Eubacterium hallii comprises the strain Eubacterium hallii DSM 3353.

32 . The method of any one of claims 1 - 14 and 18 - 31 , wherein the bacterial species Megamonas funiformis comprises the species Megamonas funiformis DSM 19343.

33 . The method of any one of claims 1 - 14 and 18 - 32 , wherein the bacterial species Megasphaera elsdenii comprises the strain Megasphaera elsdenii LC1.

34 . The method of any one of claims 1 - 14 and 18 - 33 , wherein the bacterial species Parabacteroides johnsonii comprises the strain Parabacteroides johnsonii M-165.

35 . The method of any one of claims 1 - 14 and 18 - 34 , wherein the bacterial species Butyricimonas virosa comprises the strain Butyricimonas virosa MT12.

36 . The method of any one of claims 1 - 14 and 18 - 35 , wherein the bacterial species Clostridium citroniae comprises the strain Clostridium citroniae DSM 19261.

37 . The method of any one of claims 1 - 14 and 18 - 36 , wherein the bacterial species Lactobacillus ruminis comprises the strain Lactobacillus ruminis RF3.

38 . The method of any one of claims 1 - 14 and 18 - 37 , wherein the bacterial species Methanosphaera stadtmanae comprises the strain Methanosphaera stadtmanae MCB-3.

39 . The method of any one of claims 1 - 14 and 18 - 38 , wherein the bacterial species Ruminococcus sp. comprises the strain Ruminococcus sp. 18P13.

40 . The method of any one of claims 1 - 14 and 18 - 39 , wherein the bacterial species Slackia piriformis comprises the strain Slackia piriformis DSM 22477.

41 . The method of any one of claims 1 - 14 and 18 - 40 , wherein the bacterial species Streptococcus hongkongensis comprises the strain Streptococcus hongkongensis HKU30.

42 . The method of any one of claims 3 - 14 and 18 - 41 , wherein the bacterial species improves intestinal barrier function of the subject.

43 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:1.

44 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:2.

45 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:3.

46 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:4.

47 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:5.

48 . The method of any one of claims 20 - 42 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:6.

49 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:7.

50 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:8.

51 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:9.

52 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:10.

53 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:11.

54 . The method of any one of claims 21 - 48 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:12.

55 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:13.

56 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:14.

57 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:15.

58 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:16.

59 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:17.

60 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:18.

61 . The method of any one of claims 22 - 54 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:19.

62 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:20.

63 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:21.

64 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:22.

65 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:23.

66 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:24.

67 . The method of any one of claims 23 - 61 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:25.

68 . The method of any one of claims 24 - 67 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:26.

69 . The method of any one of claims 24 - 67 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:27.

70 . The method of any one of claims 24 - 67 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:28.

71 . The method of any one of claims 25 - 70 , wherein the Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:29.

72 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:30.

73 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:31.

74 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:32.

75 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:33.

76 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:34.

77 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:35.

78 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:36.

79 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:37.

80 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:38.

81 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:39.

82 . The method of any one of claims 25 - 71 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:40.

83 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:41.

84 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:42.

85 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:43.

86 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:44.

87 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:45.

88 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:46.

89 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:47.

90 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:48.

91 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:49.

92 . The method of any one of claims 26 - 82 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:50.

93 . The method of any one of claims 27 - 92 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:51.

94 . The method of any one of claims 27 - 92 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:52.

95 . The method of any one of claims 27 - 92 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:53.

96 . The method of any one of claims 27 - 92 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:54.

97 . The method of any one of claims 28 - 96 , wherein the Clostridium sp. 40 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:57.

98 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:58.

99 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:59.

100 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:60.

101 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:61.

102 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:62.

103 . The method of any one of claims 29 - 97 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:63.

104 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:64.

105 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:65.

106 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:66.

107 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:67.

108 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:68.

109 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:69.

110 . The method of any one of claims 30 - 103 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:70.

111 . The method of any one of claims 31 - 110 , wherein the Eubacterium hallii DSM 3353 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:71.

112 . The method of any one of claims 31 - 110 , wherein the Eubacterium hallii DSM 3353 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:72.

113 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:80.

114 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:81.

115 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:82.

116 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:83.

117 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:84.

118 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:85.

119 . The method of any one of claims 32 - 112 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:86.

120 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:87.

121 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:88.

122 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:89.

123 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:90.

124 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:91.

125 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:92.

126 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:93.

127 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:94.

128 . The method of any one of claims 33 - 119 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:95.

129 . The method of any one of claims 34 - 128 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:104.

130 . The method of any one of claims 34 - 128 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:105.

131 . The method of any one of claims 34 - 128 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:106.

132 . The method of any one of claims 34 - 128 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:107.

133 . The method of any one of claims 35 - 132 , wherein the Butyricimonas virosa MT12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:55.

134 . The method of any one of claims 36 - 133 , wherein the Clostridium citroniae DSM 19261 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:56.

135 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:73.

136 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:74.

137 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:75.

138 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:76.

139 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:77.

140 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:78.

141 . The method of any one of claims 37 - 134 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:79.

142 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:96.

143 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:97.

144 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:98.

145 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:99.

146 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:100.

147 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:101.

148 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:102.

149 . The method of any one of claims 38 - 141 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:103.

150 . The method of any one of claims 39 - 149 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:108.

151 . The method of any one of claims 39 - 149 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:109.

152 . The method of any one of claims 39 - 149 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:110.

153 . The method of any one of claims 39 - 149 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:111.

154 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:112.

155 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:113.

156 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:114.

157 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:115.

158 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:116.

159 . The method of any one of claims 40 - 153 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:117.

160 . The method of any one of claims 41 - 159 , wherein the Streptococcus hongkongensis HKU30 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:118.

161 . The method of any one of claims 41 - 159 , wherein the Streptococcus hongkongensis HKU30 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:119.

162 . The method of any one of claims 3 - 14 and 18 - 161 , wherein the bacterial species in the composition is viable.

163 . The method of any one of claims 3 - 14 and 18 - 162 , wherein the bacterial strain is lyophilized.

164 . The method of any one of claims 3 - 14 and 18 - 163 , wherein the composition further comprises one or more cryopreservants.

165 . The method of any one of claims 3 - 14 and 18 - 164 , wherein the effective amount of the bacterial strain comprises at least about 1×10 3 colony forming units (CFU) of the bacterial strain.

166 . The method of any one of claims 3 - 14 and 18 - 165 , wherein the effective amount of the bacterial strain comprises about 1×10 4 to about 1×10 15 CFU of the bacterial strain.

167 . The method of any one of claims 3 - 14 and 18 - 166 , wherein the effective amount of the bacterial strain comprises about 1×10 6 to about 1×10 10 CFU of the bacterial strain.

168 . The method of any one of claims 3 - 14 and 18 - 161 , wherein the bacterial strain in the composition is non-viable.

169 . The method of claim 168 , wherein the non-viable bacterial strain is heat-killed, irradiated, or lysed.

170 . The method of any one of claims 3 - 14 and 18 - 169 , wherein the method comprises administering the composition to the subject once, twice, or three times per day.

171 . The method of any one of claims 3 - 14 and 18 - 170 , wherein the composition is formulated for oral administration.

172 . The method of any one of claims 3 - 14 and 18 - 170 , wherein the composition is formulated for rectal administration.

173 . The method of any one of claims 3 - 14 and 18 - 172 , wherein the composition is formulated as a tablet, a capsule, a powder, or a liquid.

174 . The method of any one of claims 3 - 14 and 18 - 173 , wherein the composition is formulated as a tablet.

175 . The method of claim 174 , wherein the tablet is coated.

176 . The method of claim 175 , wherein the coating comprises an enteric coating.

177 . The method of any one of claims 3 - 176 , wherein the method further comprises administering another treatment of colorectal cancer and/or other adjunct therapy to the subject.

178 . The method of claim 177 , wherein the composition comprising the bacterial strain treatment and the treatment for colorectal cancer and/or adjunct therapy are administered simultaneously.

179 . The method of claim 177 , wherein the composition comprising the bacterial strain treatment and the treatment for colorectal cancer and/or adjunct therapy are administered sequentially.

180 . The method of any one of claims 177 - 179 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises a probiotic.

181 . The method of any one of claims 177 - 179 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises surgery, radiation therapy, ablation, embolization, or a combination thereof.

182 . The method of any one of claims 177 - 179 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises a therapeutic agent.

183 . The method of claim 182 , wherein the therapeutic agent comprises a chemotherapeutic agent, targeted therapy, immunotherapy, a cell therapy, or a combination thereof.

184 . The method of claim 183 , wherein the chemotherapeutic agent comprises aflibercept, capecitabine, fluorouracil, irinotecan, leucovorin, oxaliplatin, trifluridine, tipiracil, or a combination thereof.

185 . The method of claim 183 , wherein the targeted therapy comprises bevacizumab, cetuximab, ziv-aflibercept, panitumumab, regorafenib, or a combination thereof.

186 . The method of any one of claims 183 - 185 , wherein the combination of therapeutic agents is selected from the group consisting of: FOLFOX, FOLFIRI, CAPDX, FOLFIRI-bevacizumab, FOLFIRI-cetuximab, or XELOX, and a combination thereof.

187 . The method of claim 183 , wherein the immunotherapy comprises a checkpoint inhibitor.

188 . The method of claim 187 , wherein the checkpoint inhibitor targets one or more of: CTLA-4, PD-1, PD-L1, BTLA, LAG-3, A2AR, TIM-3, B7-H3, VISTA, and IDO.

189 . The method of any one of claims 183 - 188 , wherein the composition comprising the bacterial strain further comprises the therapeutic agent.

190 . The method of claim 183 , wherein the cell therapy is a CAR T-cell therapy.

191 . The method of any one of claims 1 - 190 , wherein the subject is a human.

192 . A method for treating a subject in need thereof, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, and a combination thereof.

193 . The method of claim 192 , wherein the subject has colorectal cancer.

194 . A method for treating colorectal cancer in a subject, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, and a combination thereof.

195 . A method for treating colorectal cancer in a subject, the method comprising:
(a) detecting a dysbiosis associated with colorectal cancer in a sample from the subject; and (b) administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, and a combination thereof.

196 . The method of claim 195 , wherein the sample is a fecal sample.

197 . The method of claim 195 , wherein the sample is a biopsy sample.

198 . The method of claim 197 , wherein the biopsy sample is a colorectal biopsy sample.

199 . The method of any one of claims 195 - 198 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining bacterial gene expression in the sample from the subject.

200 . The method of any one of claims 195 - 199 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining bacterial composition in the sample from the subject.

201 . The method of claim any one of claims 195 - 200 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining that Alistipes indistinctus DSM 22520, Azotobacter sp. A1 2, Bacteroides asaccharolyticus B440, Bacteroides sp. 2_2_4 , Bilophila wadsworthia 3 1 6, Clostridium aldenense RMA9741, Clostridium bolteae DSM 15670, Clostridium lactatifermentans G17, Clostridium sp. LIP1, Desulfovibrio piger DSM 749 , Dialister pneumosintes DSM 11619, Eubacterium biforme DSM 3989, Fusobacterium mortiferum ATCC 9817 , Hungatella hathewayi 1313 , Megasphaera micronuciformis DSM 17226 , Micromonas micros ACM 5086 , Paraprevotella clara DSM 19731, Peptostreptococcus stomatis W2278, Porphyromonas somerae WAL 6690, Roseburia inulinivorans A2-194 , Ruminococcus gnavus VPI C7-9, Shigella dysenteriae CECT 584 , Subdoligranulum variabile BI-114, Veillonella alcalescens 259, or a combination thereof, is increased in the sample from subject.

202 . The method of claim any one of claims 195 - 201 , wherein detecting the dysbiosis associated with colorectal cancer comprises determining that Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, or a combination thereof, is decreased in the sample from subject.

203 . The method of claim 202 , wherein Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, or a combination thereof, is decreased in the gastrointestinal tract of the subject.

204 . A method for treating a subject in need thereof, the method comprising decreasing a population of an increased bacterial strain in the subject, wherein the increased bacterial strain is selected from the group consisting of: Alistipes indistinctus DSM 22520, Azotobacter sp. A1 2, Bacteroides asaccharolyticus B440, Bacteroides sp. 2_2_4 , Bilophila wadsworthia 3 1 6, Clostridium aldenense RMA9741, Clostridium bolteae DSM 15670, Clostridium lactatifermentans G17, Clostridium sp. LIP1, Desulfovibrio piger DSM 749 , Dialister pneumosintes DSM 11619, Eubacterium biforme DSM 3989, Fusobacterium mortiferum ATCC 9817 , Hungatella hathewayi 1313 , Megasphaera micronuciformis DSM 17226 , Micromonas micros ACM 5086 , Paraprevotella clara DSM 19731, Peptostreptococcus stomatis W2278, Porphyromonas somerae WAL 6690, Roseburia inulinivorans A2-194 , Ruminococcus gnavus VPI C7-9, Shigella dysenteriae CECT 584 , Subdoligranulum variabile BI-114, Veillonella alcalescens 259, and a combination thereof.

205 . The method of claim 204 , wherein the subject has colorectal cancer.

206 . The method of claim 204 or 205 , wherein decreasing the population of an increased bacterial strain comprises administering to the subject a bacteriophage.

207 . The method of any one of claims 204 - 206 , wherein decreasing the population of an increased bacterial strain comprises administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Bacteroides eggerthii 1 2 48FAA, Bacteroides eggerthii CCUG 9559, Bacteroides goldsteinii ATCC BAA 1180, Bacteroides pectinophilus N3, Bacteroides plebeius M12, Bacteroides vulgatus 8482 , Barnesiella intestinihominis DSM 21032, Bifidobacterium stercoris EG1, Clostridium sp. 40, Clostridium spiroforme CCM 6168, Eubacterium eligens DSM 3376, Eubacterium hallii DSM 3353 , Megamonas funiformis DSM 19343 , Megasphaera elsdenii LC1 , Parabacteroides johnsonii M-165 , Butyricimonas virosa MT12, Clostridium citroniae DSM 19261, Lactobacillus ruminis RF3 , Methanosphaera stadtmanae MCB-3 , Ruminococcus sp. 18P13 , Slackia piriformis DSM 22477, Streptococcus hongkongensis HKU30, and a combination thereof.

208 . The method of any one of claims 192 - 203 and 205 - 207 , wherein the colorectal cancer is adenocarcinoma, a carcinoid tumor, a gastrointestinal stromal tumor, or lymphoma.

209 . The method of any one of claims 192 - 203 and 207 - 208 , wherein the bacterial strain comprises Bacteroides eggerthii 1 2 48FAA.

210 . The method of any one of claims 192 - 203 and 207 - 209 , wherein the bacterial strain comprises Bacteroides eggerthii CCUG 9559.

211 . The method of any one of claims 192 - 203 and 207 - 210 , wherein the bacterial strain comprises Bacteroides goldsteinii ATCC BAA 1180.

212 . The method of any one of claims 192 - 203 and 207 - 211 , wherein the bacterial strain comprises Bacteroides pectinophilus N3.

213 . The method of any one of claims 192 - 203 and 207 - 212 , wherein the bacterial strain comprises Bacteroides plebeius M12.

214 . The method of any one of claims 192 - 203 and 207 - 213 , wherein the bacterial strain comprises Bacteroides vulgatus 8482.

215 . The method of any one of claims 192 - 203 and 207 - 214 , wherein the bacterial strain comprises Barnesiella intestinihominis DSM 21032.

216 . The method of any one of claims 192 - 203 and 207 - 215 , wherein the bacterial strain comprises Bifidobacterium stercoris EG1.

217 . The method of any one of claims 192 - 203 and 207 - 216 , wherein the bacterial strain comprises Clostridium sp. 40.

218 . The method of any one of claims 192 - 203 and 207 - 217 , wherein the bacterial strain comprises Clostridium spiroforme CCM 6168.

219 . The method of any one of claims 192 - 203 and 207 - 218 , wherein the bacterial strain comprises Eubacterium eligens DSM 3376.

220 . The method of any one of claims 192 - 203 and 207 - 219 , wherein the bacterial strain comprises Eubacterium hallii DSM 3353.

221 . The method of any one of claims 192 - 203 and 207 - 220 , wherein the bacterial strain comprises Megamonas funiformis DSM 19343.

222 . The method of any one of claims 192 - 203 and 207 - 221 , wherein the bacterial strain comprises Megasphaera elsdenii LC1.

223 . The method of any one of claims 192 - 203 and 207 - 222 , wherein the bacterial strain comprises Parabacteroides johnsonii M-165.

224 . The method of any one of claims 192 - 203 and 207 - 223 , wherein the bacterial strain comprises Butyricimonas virosa MT12.

225 . The method of any one of claims 192 - 203 and 207 - 224 , wherein the bacterial strain comprises Clostridium citroniae DSM 19261.

226 . The method of any one of claims 192 - 203 and 207 - 225 , wherein the bacterial strain comprises Lactobacillus ruminis RF3.

227 . The method of any one of claims 192 - 203 and 207 - 226 , wherein the bacterial strain comprises Methanosphaera stadtmanae MCB-3.

228 . The method of any one of claims 192 - 203 and 207 - 227 , wherein the bacterial strain comprises Ruminococcus sp. 18P13.

229 . The method of any one of claims 192 - 203 and 207 - 228 , wherein the bacterial strain comprises Slackia piriformis DSM 22477.

230 . The method of any one of claims 192 - 203 and 207 - 229 , wherein the bacterial strain comprises Streptococcus hongkongensis HKU30.

231 . The method of any one of claims 192 - 203 and 207 - 230 , wherein the bacterial strain improves intestinal barrier function of the subject.

232 . The method of any one of claims 192 - 203 and 207 - 231 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:1.

233 . The method of any one of claims 192 - 203 and 207 - 232 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:2.

234 . The method of any one of claims 192 - 203 and 207 - 233 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:3.

235 . The method of any one of claims 192 - 203 and 207 - 234 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:4.

236 . The method of any one of claims 192 - 203 and 207 - 235 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:5.

237 . The method of any one of claims 192 - 203 and 207 - 236 , wherein the Bacteroides eggerthii 1 2 48FAA has a 16S RNA gene that is at least 95% identical to SEQ ID NO:6.

238 . The method of any one of claims 192 - 203 and 207 - 237 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:7.

239 . The method of any one of claims 192 - 203 and 207 - 238 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:8.

240 . The method of any one of claims 192 - 203 and 207 - 239 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:9.

241 . The method of any one of claims 192 - 203 and 207 - 240 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:10.

242 . The method of any one of claims 192 - 203 and 207 - 241 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:11.

243 . The method of any one of claims 192 - 203 and 207 - 242 , wherein the Bacteroides eggerthii CCUG 9559 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:12.

244 . The method of any one of claims 192 - 203 and 207 - 243 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:13.

245 . The method of any one of claims 192 - 203 and 207 - 244 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:14.

246 . The method of any one of claims 192 - 203 and 207 - 245 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:15.

247 . The method of any one of claims 192 - 203 and 207 - 246 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:16.

248 . The method of any one of claims 192 - 203 and 207 - 247 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:17.

249 . The method of any one of claims 192 - 203 and 207 - 248 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:18.

250 . The method of any one of claims 192 - 203 and 207 - 249 , wherein the Bacteroides goldsteinii ATCC BAA 1180 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:19.

251 . The method of any one of claims 192 - 203 and 207 - 250 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:20.

252 . The method of any one of claims 192 - 203 and 207 - 251 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:21.

253 . The method of any one of claims 192 - 203 and 207 - 252 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:22.

254 . The method of any one of claims 192 - 203 and 207 - 253 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:23.

255 . The method of any one of claims 192 - 203 and 207 - 254 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:24.

256 . The method of any one of claims 192 - 203 and 207 - 255 , wherein the Bacteroides pectinophilus N3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:25.

257 . The method of any one of claims 192 - 203 and 207 - 256 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:26.

258 . The method of any one of claims 192 - 203 and 207 - 257 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:27.

259 . The method of any one of claims 192 - 203 and 207 - 258 , wherein the Bacteroides plebeius M12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:28.

260 . The method of any one of claims 192 - 203 and 207 - 259 , wherein the Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:29.

261 . The method of any one of claims 192 - 203 and 207 - 260 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:30.

262 . The method of any one of claims 192 - 203 and 207 - 261 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:31.

263 . The method of any one of claims 192 - 203 and 207 - 262 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:32.

264 . The method of any one of claims 192 - 203 and 207 - 263 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:33.

265 . The method of any one of claims 192 - 203 and 207 - 264 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:34.

266 . The method of any one of claims 192 - 203 and 207 - 265 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:35.

267 . The method of any one of claims 192 - 203 and 207 - 266 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:36.

268 . The method of any one of claims 192 - 203 and 207 - 267 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:37.

269 . The method of any one of claims 192 - 203 and 207 - 268 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:38.

270 . The method of any one of claims 192 - 203 and 207 - 269 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:39.

271 . The method of any one of claims 192 - 203 and 207 - 270 , Bacteroides vulgatus 8482 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:40.

272 . The method of any one of claims 192 - 203 and 207 - 271 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:41.

273 . The method of any one of claims 192 - 203 and 207 - 272 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:42.

274 . The method of any one of claims 192 - 203 and 207 - 273 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:43.

275 . The method of any one of claims 192 - 203 and 207 - 274 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:44.

276 . The method of any one of claims 192 - 203 and 207 - 275 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:45.

277 . The method of any one of claims 192 - 203 and 207 - 276 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:46.

278 . The method of any one of claims 192 - 203 and 207 - 277 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:47.

279 . The method of any one of claims 192 - 203 and 207 - 278 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:48.

280 . The method of any one of claims 192 - 203 and 207 - 279 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:49.

281 . The method of any one of claims 192 - 203 and 207 - 280 , wherein the Barnesiella intestinihominis DSM 21032 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:50.

282 . The method of any one of claims 192 - 203 and 207 - 281 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:51.

283 . The method of any one of claims 192 - 203 and 207 - 282 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:52.

284 . The method of any one of claims 192 - 203 and 207 - 283 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:53.

285 . The method of any one of claims 192 - 203 and 207 - 284 , wherein the Bifidobacterium stercoris EG1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:54.

286 . The method of any one of claims 192 - 203 and 207 - 285 , wherein the Clostridium sp. 40 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:57.

287 . The method of any one of claims 192 - 203 and 207 - 286 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:58.

288 . The method of any one of claims 192 - 203 and 207 - 287 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:59.

289 . The method of any one of claims 192 - 203 and 207 - 288 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:60.

290 . The method of any one of claims 192 - 203 and 207 - 289 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:61.

291 . The method of any one of claims 192 - 203 and 207 - 290 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:62.

292 . The method of any one of claims 192 - 203 and 207 - 291 , wherein the Clostridium spiroforme CCM 6168 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:63.

293 . The method of any one of claims 192 - 203 and 207 - 292 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:64.

294 . The method of any one of claims 192 - 203 and 207 - 293 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:65.

295 . The method of any one of claims 192 - 203 and 207 - 294 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:66.

296 . The method of any one of claims 192 - 203 and 207 - 295 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:67.

297 . The method of any one of claims 192 - 203 and 207 - 296 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:68.

298 . The method of any one of claims 192 - 203 and 207 - 297 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:69.

299 . The method of any one of claims 192 - 203 and 207 - 298 , wherein the Eubacterium eligens DSM 3376 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:70.

300 . The method of any one of claims 192 - 203 and 207 - 299 , wherein the Eubacterium hallii DSM 3353 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:71.

301 . The method of any one of claims 192 - 203 and 207 - 300 , wherein the Eubacterium hallii DSM 3353 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:72.

302 . The method of any one of claims 192 - 203 and 207 - 301 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:80.

303 . The method of any one of claims 192 - 203 and 207 - 302 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:81.

304 . The method of any one of claims 192 - 203 and 207 - 303 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:82.

305 . The method of any one of claims 192 - 203 and 207 - 304 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:83.

306 . The method of any one of claims 192 - 203 and 207 - 305 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:84.

307 . The method of any one of claims 192 - 203 and 207 - 306 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:85.

308 . The method of any one of claims 192 - 203 and 207 - 307 , wherein the Megamonas funiformis DSM 19343 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:86.

309 . The method of any one of claims 192 - 203 and 207 - 308 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:87.

310 . The method of any one of claims 192 - 203 and 207 - 309 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:88.

311 . The method of any one of claims 192 - 203 and 207 - 310 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:89.

312 . The method of any one of claims 192 - 203 and 207 - 311 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:90.

313 . The method of any one of claims 192 - 203 and 207 - 312 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:91.

314 . The method of any one of claims 192 - 203 and 207 - 313 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:92.

315 . The method of any one of claims 192 - 203 and 207 - 314 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:93.

316 . The method of any one of claims 192 - 203 and 207 - 315 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:94.

317 . The method of any one of claims 192 - 203 and 207 - 316 , wherein the Megasphaera elsdenii LC1 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:95.

318 . The method of any one of claims 192 - 203 and 207 - 317 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:104.

319 . The method of any one of claims 192 - 203 and 207 - 318 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:105.

320 . The method of any one of claims 192 - 203 and 207 - 319 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:106.

321 . The method of any one of claims 192 - 203 and 207 - 320 , wherein the Parabacteroides johnsonii M 165 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:107.

322 . The method of any one of claims 192 - 203 and 207 - 321 , wherein the Butyricimonas virosa MT12 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:55.

323 . The method of any one of claims 192 - 203 and 207 - 322 , wherein the Clostridium citroniae DSM 19261 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:56.

324 . The method of any one of claims 192 - 203 and 207 - 323 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:73.

325 . The method of any one of claims 192 - 203 and 207 - 324 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:74.

326 . The method of any one of claims 192 - 203 and 207 - 325 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:75.

327 . The method of any one of claims 192 - 203 and 207 - 326 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:76.

328 . The method of any one of claims 192 - 203 and 207 - 327 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:77.

329 . The method of any one of claims 192 - 203 and 207 - 328 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:78.

330 . The method of any one of claims 192 - 203 and 207 - 329 , wherein the Lactobacillus ruminis RF3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:79.

331 . The method of any one of claims 192 - 203 and 207 - 330 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:96.

332 . The method of any one of claims 192 - 203 and 207 - 331 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:97.

333 . The method of any one of claims 192 - 203 and 207 - 332 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:98.

334 . The method of any one of claims 192 - 203 and 207 - 333 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:99.

335 . The method of any one of claims 192 - 203 and 207 - 334 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:100.

336 . The method of any one of claims 192 - 203 and 207 - 335 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:101.

337 . The method of any one of claims 192 - 203 and 207 - 336 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:102.

338 . The method of any one of claims 192 - 203 and 207 - 337 , wherein the Methanosphaera stadtmanae MCB-3 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:103.

339 . The method of any one of claims 192 - 203 and 207 - 338 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:108.

340 . The method of any one of claims 192 - 203 and 207 - 339 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:109.

341 . The method of any one of claims 192 - 203 and 207 - 340 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:110.

342 . The method of any one of claims 192 - 203 and 207 - 341 , wherein the Ruminococcus sp. 18P13 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:111.

343 . The method of any one of claims 192 - 203 and 207 - 342 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:112.

344 . The method of any one of claims 192 - 203 and 207 - 343 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:113.

345 . The method of any one of claims 192 - 203 and 207 - 344 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:114.

346 . The method of any one of claims 192 - 203 and 207 - 345 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:115.

347 . The method of any one of claims 192 - 203 and 207 - 346 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:116.

348 . The method of any one of claims 192 - 203 and 207 - 347 , wherein the Slackia piriformis DSM 22477 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:117.

349 . The method of any one of claims 192 - 203 and 207 - 348 , wherein the Streptococcus hongkongensis HKU30 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:118.

350 . The method of any one of claims 192 - 203 and 207 - 349 , wherein the Streptococcus hongkongensis HKU30 has a 16S RNA gene that is at least 95% identical to SEQ ID NO:119.

351 . The method of any one of claims 192 - 203 and 207 - 350 , wherein the bacterial strain in the composition is viable.

352 . The method of any one of claims 192 - 203 and 207 - 351 , wherein the bacterial strain is lyophilized.

353 . The method of any one of claims 192 - 203 and 207 - 352 , wherein the composition further comprises one or more cryopreservants.

354 . The method of any one of claims 192 - 203 and 207 - 353 , wherein the effective amount of the bacterial strain comprises at least about 1×10 3 colony forming units (CFU) of the bacterial strain.

355 . The method of any one of claims 192 - 203 and 207 - 354 , wherein the effective amount of the bacterial strain comprises about 1×10 4 to about 1×10 15 CFU of the bacterial strain.

356 . The method of any one of claims 192 - 203 and 207 - 355 , wherein the effective amount of the bacterial strain comprises about 1×10 6 to about 1×10 10 CFU of the bacterial strain.

357 . The method of any one of claims 192 - 203 and 207 - 350 , wherein the bacterial strain in the composition is non-viable.

358 . The method of claim 357 , wherein the non-viable bacterial strain is heat-killed, irradiated, or lysed.

359 . The method of any one of claims 192 - 203 and 207 - 358 , wherein the method comprises administering the composition to the subject once, twice, or three times per day.

360 . The method of any one of claims 192 - 203 and 207 - 359 , wherein the composition is formulated for oral administration.

361 . The method of any one of claims 192 - 203 and 207 - 359 , wherein the composition is formulated for rectal administration.

362 . The method of any one of claims 192 - 203 and 207 - 361 , wherein the composition is formulated as a tablet, a capsule, a powder, or a liquid.

363 . The method of any one of claims 192 - 203 and 207 - 361 , wherein the composition is formulated as a tablet.

364 . The method of claim 363 , wherein the tablet is coated.

365 . The method of claim 364 , wherein the coating comprises an enteric coating.

366 . The method of any one of claims 192 - 203 and 207 - 365 , wherein the method further comprises administering another treatment of colorectal cancer and/or other adjunct therapy to the subject.

367 . The method of claim 366 , wherein the composition comprising the bacterial strain treatment and the treatment for colorectal cancer and/or adjunct therapy are administered simultaneously.

368 . The method of claim 366 , wherein the composition comprising the bacterial strain treatment and the treatment for colorectal cancer and/or adjunct therapy are administered sequentially.

369 . The method of any one of claims 366 - 368 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises a probiotic.

370 . The method of any one of claims 366 - 368 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises surgery, radiation therapy, ablation, embolization, or a combination thereof.

371 . The method of any one of claims 366 - 368 , wherein the treatment for colorectal cancer and/or adjunct therapy comprises a therapeutic agent.

372 . The method of claim 371 , wherein the therapeutic agent comprises a chemotherapeutic agent, targeted therapy, immunotherapy, a cell therapy, or a combination thereof.

373 . The method of claim 372 , wherein the chemotherapeutic agent comprises aflibercept, capecitabine, fluorouracil, irinotecan, leucovorin, oxaliplatin, trifluridine, tipiracil, or a combination thereof.

374 . The method of claim 372 , wherein the targeted therapy comprises bevacizumab, cetuximab, ziv-aflibercept, panitumumab, regorafenib, or a combination thereof.

375 . The method of claim 372 , wherein the combination of therapeutic agents is selected from the group consisting of: FOLFOX, FOLFIRI, CAPDX, FOLFIRI-bevacizumab, FOLFIRI-cetuximab, or XELOX, and a combination thereof.

376 . The method of claim 372 , wherein the immunotherapy comprises a checkpoint inhibitor.

377 . The method of claim 376 , wherein the checkpoint inhibitor targets one or more of: CTLA-4, PD-1, PD-L1, BTLA, LAG-3, A2AR, TIM-3, B7-H3, VISTA, and IDO.

378 . The method of any one of claims 371 - 377 , wherein the composition comprising the bacterial strain further comprises the therapeutic agent.

379 . The method of claim 372 , wherein the cell therapy is a CAR T-cell therapy.

380 . The method of any one of claims 192 - 379 , wherein the subject is a human.

Cited by (0)

No later patents cite this yet.

References (0)

No backward citations on record.